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WIP

WIP #12

Workflow file for this run

name: "Lassa workflow"
on:
- push
- pull_request
jobs:
lassa:
permissions:
contents: read
id-token: write
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: r-lib/actions/setup-r@v2
with:
# use-public-rspm: true
# https://ropensci.r-universe.dev
extra-repositories: |
https://mrc-ide.r-universe.dev
- uses: r-lib/actions/setup-r-dependencies@v2
with:
packages: |
mrc-ide/orderly.sharedfile
mrc-ide/epireview
cowplot
doconv
dplyr
epitrix
estmeansd
flextable
ftExtra
ggbreak
ggforce
ggplot2
ggrepel
ggsci
ggspatial
grid
gridExtra
gt
harrypotter
ids
janitor
meta
metafor
mixdist
odbc
officer
optparse
patchwork
png
purrr
ragg
readr
readxl
rio
rnaturalearth
rnaturalearthdata
scales
sf
snakecase
splitstackshape
stringr
tibble
tidyr
tidyverse
tm
writexl
zip
- uses: mrc-ide/orderly-action@main
with:
packit-url: https://packit.dide.ic.ac.uk/priority-pathogens
- shell: Rscript {0}
run: |
library(orderly2)
orderly_location_pull_packet("latest(name == 'db_extraction' && parameter:pathogen == 'LASSA')",
options = list(location="packit"))
ids <- c(
orderly_run("db_double", parameters = list(pathogen = "LASSA")),
orderly_run("db_compilation", parameters = list(pathogen = "LASSA")),
orderly_run("lassa_serology", parameters = list(pathogen = "LASSA")),
orderly_run("lassa_severity", parameters = list(pathogen = "LASSA")),
orderly_run("lassa_delays", parameters = list(pathogen = "LASSA")),
orderly_run("lassa_transmission", parameters = list(pathogen = "LASSA")),
orderly_run("lassa_summary", parameters = list(pathogen = "LASSA")),
orderly_run("lassa_latex_tables", parameters = list(pathogen = "LASSA")),
orderly_run("lassa_collate", parameters = list(pathogen = "LASSA")))
orderly_location_push(ids, "packit")